Scheduled MS3 for Quantitation

A method for scheduled mass spectrometry/mass spectrometry/mass spectrometry (MS3), comprising:

• separating a compound of interest from a sample over a known time period using a separation device;
• performing a plurality of scheduled multiple reaction monitoring (sMRM) experiments over the known time period on the separating compound of interest using a mass spectrometer, producing an intensity of a product ion of the compound of interest for each of the plurality of sMRM experiments;
• receiving each intensity for the product ion for each of the plurality of sMRM experiments from the mass spectrometer using a processor;
• comparing each intensity for the product ion for each of the plurality of sMRM experiments to a threshold intensity level using the processor, and
• when an intensity for the product ion of an sMRM experiment of the plurality of sMRM experiments is equal to or exceeds the threshold intensity level, instructing the mass spectrometer to perform one or more MS3 experiments for the product ion using the processor, producing intensities of one or more secondary fragment ions of the compound of interest for each of the one or more MS3 experiments.

A computer program product, comprising a non-transitory and tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor so as to perform a method for scheduled mass spectrometry/mass spectrometry/mass spectrometry (MS3), the method comprising:

• providing a system, wherein the system comprises one or more distinct software modules, and wherein the distinct software modules comprise an analysis module and a control module;
• receiving an intensity for a product ion for each of a plurality of scheduled multiple reaction monitoring (sMRM) experiments the plurality of sMRM experiments from a mass spectrometer using the analysis module, wherein each intensity for the product ion of each of the plurality of sMRM experiments is produced by performing the plurality of sMRM experiments over a known time period on a separating compound of interest using a mass spectrometer, and wherein the separating compound of interest is separated from a sample over the known time period using a separation device;
• performing a plurality of scheduled multiple reaction monitoring (sMRM) experiments, producing an intensity of a product ion of the compound of interest for each of the plurality of sMRM experiments;
• comparing each intensity for the product ion for each of the plurality of sMRM experiments to a threshold intensity level using the control module;
• and
• when an intensity for the product ion of an sMRM experiment of the plurality of sMRM experiments is equal to or exceeds the threshold intensity level, instructing the mass spectrometer to perform one or more MS3 experiments for the product ion using the control module, producing intensities of one or more secondary fragment ions of the compound of interest for each of the one or more MS3 experiments.